Code Lyoko: Paradox
by Metal Hunter
Summary: Not really good at summaries, but here it goes. A new fight begins, new heroes join the ranks and the timeline is change forever. My own characters will appear later. Well Enjoy!
1. Chapter 1

**Code Lyoko: ****Paradox**

**Authors ****Note: My first Lyoko Fanfic! Its episode based, meaning that each chapter counts as one episode. This story continues on after the final episode of season 4. Well I hope you enjoy it!**

**Episode 1 (Or Episode 96): Return of the evil**

Aelita lay on her bed, staring at the ceiling. It had been 3 months since they had shut down the supercomputer and vanquished Xana. Since then Aelita had been having nightmares practically every night since. Every night was a re-enactment of the final fight against Xana, each concluding with her father dying. Every night, she tries to stop it from happening, but fails.

In the following morning, everybody was in the canteen having breakfast, while Aelita explained her nightmares to them.

"Every night I have this same nightmare. I'm at the Celestrial Dome, with my Father being attack by two Mantas. I refuse to activate the program and instead try to protect my Father. Eventually I have to activate the program and he dies."

"Well its natural, to see someone you love die and then have nightmares about it." answered Yumi but she wasn't even sure if it was the right thing to say.

"I never felt so helpless in my entire life. He was going to die and I couldn't help him." Aelita responded starting to weep.

"Well thanks to you and your Father, we don't need to worry about Xana attacks anymore!" said Odd trying to lighten the mood.

"Look Aelita. We can still keep searching for Franz Hopper. We can go to the factory and search for him." Jeremie knew that it was still possible that Franz could have survived the attack. He had done it before, when he revived Aelita.

"No." said Aelita looking even worse than before. "We can't risk turning on the Supercomputer without the possibility of Xana returning!"

"But we won. We defeated Xana." responded Ulrich. He then realized that he should have chosen his words more carefully.

"WON?!" reacted Aelita almost shouting in anger. "Don't you care that someone has lost their life? And all you can selfishly think of, is that we won?!" She then stormed out of the lunch room. Once Aelita was out of there, she started to run and tears began to trickle down her face.

Immediately after Aelita had left, Ulrich ran out of the Lunch room and looked around to see if he could find out where she had gone to. He now wished he had waited a little longer to select the correct words from his head. He was trying to prove to her that they could start up the Supercomputer again, but it came out wrongly. And now he couldn't even apologize!

Deep within the factory, nothing was active. It had been like this for 3 months since the supercomputer had been turned off. On the bottom level however, the mark of Xana engraved hatch opened and the supercomputer rose like a phoenix rising from the ashes. Something in the past wasn't going to stay dead.

Aelita lay next to a tree, weeping her heart out. She had no family or relatives in this world. She didn't even really exist here. Was there any point of living here anymore? She broke down into tears of pain and sorrow.

_Aelita._

Aelita stopped crying and sat up. She looked around for anyone else but couldn't see anybody. "Who's there?" she asked not really knowing whether to expect an answer or not.

_Aelita, my dear, I have returned._

Aelita soon remembered the familiar voice. "Daddy? Is that you?" Tears were starting to drip from her eyes. "I thought that you died!"

_I still live… but very weak. __You need to come to me and find me on Lyoko._

Aelita was unsure about this. She first thought that it was Xana, but then realized it couldn't be him because he was destroyed. She put a hand to her forehead and closed her eyes. She could have been just hallucinating the whole thing.

_I…need you to find… me. I… love…_

"Daddy…" Aelita waited a couple of minutes. Nothing came. She got up and started to head towards the factory but then stopped. Should she tell her friends? She then thought of Ulrich. He would probably not talk to her, after what she had said to him. No she wouldn't tell them. Xana was gone so there wasn't any threat and she might have just imagined it. With her father possibly in trouble, she ran towards the sewer entrance.

Ulrich was now on the verge of giving up. He had spent the whole of the morning searching everywhere for Aelita and had now decided that he would have to apologize to her at lunch or possibly dinner. Ulrich started to wonder whether Aelita would ever forgive him or even speak to him again. He saw Sissi walking in the opposite direction.

"Hey Sissi," called Ulrich. Maybe she had seen Aelita.

"Oh hey Ulrich! So how are you?" Sissi was happy that Ulrich's group had finally accepted her and talked to her.

"Have you seen Aelita at all today?"

"No not really, why?"

"Uh nothing…" answered Ulrich, wondering where Aelita could be.

Meanwhile, Jeremie and Odd were in Jeremy's room. Odd was being tutored on Biology, which he had actually requested personally, because of his incredibly low test score. It was so bad that Ulrich did better than him in the latest test!

"So what is Photosynthesis?" Jeremie was asking a quiz on what Odd should have studied.

"Uhh… Photosynthesis is…" began Odd. What was photosynthesis anyway? "Photosynthesis is the way that plants take in sunshine and produces energy."

"Correct but how does it work?" Jeremie had his doubts that Odd really knew what he was talking about.

"Umm…" Odd was about to answer when he was interrupted by several bleeps coming from a packed away laptop. _Phew saved by the Laptop,_ thought Odd as Jeremie picked up and unfolded the persistently bleeping laptop.

"Huh? That can't be right," said Jeremie as looked at the different screens "It says that there's an activated tower on Lyoko!"

"There's 2 things wrong with that." Odd was confused as much as Jeremie. "1. We destroyed Xana and 2. We shut down the supercomputer!"

"I don't know but someone must have turned on the supercomputer."

"Who else knows about the supercomputer? And why reactivate it?" A smile was creeping onto Odd's face. This was what he wanted. Action and being a hero!

"We better head over there and find out. You call Yumi and I'll call Ulrich!" They both ran out of the room and headed for the Gym entrance.

Aelita arrived at the computer lab. She went straight over to the interface and started looking for her father. She was so focused on her mission, that Aelita didn't notice the electric ghost starting to appear behind her. It surrounded Aelita and started to choke her. Aelita then fell to the floor knocked out. The spectre then took her down a level and placed Aelita in the scanner. It then went back up to the lab and activated a virtualization process to Lyoko. Down a level, the scanner blared into life. It scanned and virtualized the atoms of Aelita in seconds. The scanner doors then opened with a burst of light as if nothing had happened. Aelita appeared on Lyoko in the Carthage and fell to the floor. A dark figure walked into the arena. He looked down at the unconscious Aelita and raised his hand. Dark smoke flowed out of his hand and surrounded Aelita. He slowly lifted her up and carried her off into the depths of Sector 5.

The rest of the group was running towards the factory. They had spent a lot of time to get rid of Xana and now they might have a new threat. Worst of all they didn't know whether Aelita was safe. They rode the lift down to the lab. Jeremie immediately ran towards computer terminal and quickly searched the readouts.

"Huh?" He stared puzzled at the screen. "Aelita is virtualized on Lyoko, in Sector 5. Why would she virtualize herself there?" Jeremie then tried contacting her, but to no avail.

"Maybe she just wanted to get away from it all." suggested Yumi. "It's always been a home to her."

"Yeah or she's been kidnapped!" Ulrich knew Aelita wouldn't turn the supercomputer back on just for a vacation.

"But by who? Xana was destroyed!" Jeremie was certain, more than anyone else, that this was the case!

"Just send us then. We'll track Aelita down and talk to her!" Odd secretly wanted to go back to Lyoko, just once more.

Hmm…" Jeremie glanced back at the read out. The tower that was activated had mysteriously deactivated itself. "Ok, but be careful. Head down to the scanner room and I'll start the virtualization process." Then Odd, Ulrich and Yumi boarded the elevator and descended down to the scanner room.

Aelita awoke and looked around at her surroundings. The light blue walls of the Carthage covered most of her view. Aelita then tried to get up… or even move, but she couldn't. Her body wasn't responding. She looked down and saw that most of her was covered by a dark fog. Then he arrived. He wore black armor and had dark red hair. On the front of his armor and on his forehead, there was the unmistakable mark of Xana. He walked over to Aelita and stared at her with his black eyes. Aelita stared back, while trembling with fear.

"Are you one of Xana`s warriors?" she asked, still drenched with terror. "But how is that possible, Xana was destroyed."

"I am all that is left of him. He is severely weakened." responded the warrior. "You are the key to his survival and eventual victory!"

"I will never help Xana!" Aelita shouted in protest.

"He doesn't need you, but what is inside of you." Then he made a smile which made Aelita even more uneasy. "Since the lord Xana is so weak, he couldn't create another Scyphozoa, so we'll have to extract the data in a more painful way." the warrior smirked. He then placed his hand just above her forehead. Then a beam of red light came from his palm and projected a mark of Xana onto Aelita's forehead. The red aura then surrounded her body. Aelita screamed. She had never felt such pain and agony throughout her entire body. It was impossible to describe. She felt as though her very atoms were being torn apart. The warrior simply smiled and continued his search.

Odd, Ulrich and Yumi landed in the Carthage arena. They immediately heard screams. Of Torment and Suffering. Aelita! "Jeremie! Aelita is in danger. Can you locate her?" Ulrich asked feeling more guilt than he had ever felt before. Aelita was in danger and it was his fault!

"Start moving!" Jeremie barked. "I'll direct you once you are in the Core Zone." He then wiped the sweat off his brow, as he searched the Carthage for girl who he loved. The corridor seemed to take an eternity. The Lyoko Warriors reached a junction. There were three separate paths. "What way Einstein?" Odd shouted, tapping his foot impatiently.

"I…I don't know." came Jeremie's voice, agitated by something. "Her signal is unstable and I can't get a lock on it." There was feeling of hopelessness coming from his voice. Yumi, sensing that Jeremie was feeling the pressure, took charge.

"Well… there are three passages, so if we each take one and at least one of us will find Aelita!" They each then took their separate ways, each hoping to find Aelita.

The dark warrior laughed maniacally! He had finally found what he was looking for. The bits of data were ripped from Aelita. Or what was left of her. She now could not even speak for the agony. Aelita then passed out. The last pieces of data were absorbed into the warrior's hand.

"Thank you for being so cooperative, Aelita." The warrior spoke to her face sarcastically. "Xana said you would be difficult, but those rumors are completely untrue! But now, I have to leave you." He kissed her cheek. "You just can't live without me though, can you?" He laughed again. This time, though, he raised his barbed broadsword. "Farewell, Miss Stones!" The sword came down.

And hit two katana. Ulrich had made it. It was close. Too close. As the dark warrior had raised his sword, Ulrich had arrived in the room. He had then raced across (jumping over Aelita) and with his swords drawn, blocked the to-be-fatal blow. The warrior's smile vanished.

"Ulrich Stern…" he acknowledged. "You just had to come and spoil my fun, didn't you?"

"Of course." smirked Ulrich. The swords clashed again. The dark warrior backed and came in with another powerful strike. Ulrich ducked to the left, avoiding the blow, and pushed his two katana forward. The Xana warrior saw it coming and quickly moved his broad sword, blocking the attack. With a sweeping kick, The Xana warrior brings Ulrich to the ground. The two katana scattered across the floor.

"Ha ha ha! Nice try Lyoko Warrior but I was better!" Gloated the warrior. He raised his broadsword over his head. "With you out of the way then nothing can stop me from killing Miss Stones! So long, Mr. Stern!" The warrior was knocked back by three laser arrows. Yumi and Odd had arrived just in time!

"Go back to Xana, creep!" Yumi was readying her twin Tessen fans. Odd was also aimed for another volley of laser arrows.

"I got what I needed from Aelita, Lyoko Warriors!" shouted the Xana warrior, triumphantly, "You cannot stop Xana now!" He suddenly disappeared into a streak of black smoke.

Ulrich got to his feet and ran over to Aelita, holding her in his arms.

"Aelita! Aelita are you ok?" No response came. Had he been too late? Was she gone forever? "Please wake up!" Yumi said nothing, just watched in shock.

"Einstein, is Aelita still alive?!" Odd was just as worried as the others. Then Aelita stirred. She tried to speak but… she couldn't.

"Jeremie, I think Aelita wants to be materialized." Ulrich then looked down to the girl in his arms. She looked as though, if on Earth, she could cry a waterfall of tears.

Back on Earth, the Lyoko Warriors discussed what Xana had taken from Aelita. Aelita was resting against a wall. Even though she had been materialized without a scratch, she was still in agony. Also she had no voice to discuss with! In screaming so much, because of the pain, she had lost her voice.

"Have you found out what that Xana warrior took from Aelita, Jeremie?" Yumi asked while glancing over at Aelita resting.

"I don't know," responded Jeremie "and that's what worries me."

"It seems like a last ditch attempt for Xana." Ulrich knew that Xana was still incredibly weakened. "He would only do something like this, if he knew that it could allow him to defeat us."

Odd was looking puzzled. "But we already destroyed Xana… Didn't we?"

"The multi-agent program managed to wipe out the majority of the Xana agents but some may have survived." This worried Jeremie because any one of the smaller Xana remains could become a new Xana. He then sighed and went back to face the interface screen. "I'll stay here this afternoon and tonight. I'll try to find out what was taken from Aelita."

Yumi nodded. "Ok. I think the best thing for Aelita is to go back to Kadic and get some rest." They all agreed on that. Ulrich walked over and let Aelita lean on his shoulder as she got to her feet. She winced in pain. They both then moved over to the elevator.

"See you tomorrow, Einstein." Odd waved as he boarded the elevator.

"Yeah, see you Jeremie." seconded Ulrich. He wasn't worried about Jeremie, because he used to always stay overnight at the factory and often missed lunch and dinner.

When they got out side, they were hit by a cool late afternoon breeze. They had unfortunately missed lunch, which Odd immediately pointed out, but at least they still had five member of the group. On the bridge, Ulrich looked up at Aelita, who he was still supporting.

"Aelita, I'm truly sorry about our argument this Morning." She immediately stared back at him. "All I was trying to point out was that, it was ok to turn on the supercomputer because Xana was destroyed and search for your father." Aelita smiled slightly. She prepared to speak but nothing came once again, just a half-choked indication of joy, nearly falling over in the process. Ulrich grabbed her as she slipped.

"Easy. Don't hurt yourself trying to respond." He was worried about Aelita and didn't want her to get hurt again because of him. Her smile was a good enough indication for him.

After been escorted back to her room, Aelita immediately went to lie down on her bed. She wished the agony would go away. She was happy that Ulrich was talking to her again. Aelita then thought of the Xana Warrior and Xana being revived. Her father had died for nothing. With this thought, she wept herself to sleep.

**Authors Note: That's the end of the First Chapter! I'll try to keep up a routine of posting of Fridays but if not, I try to get another chapter soon.**


	2. Chapter 2

**Authors Note: Thanks to ****everybody who has commented. I apologies for the lack of updates but my laptop broke. I've been slowly writing this chapter up and I'm planning to take it at my own pace for just now anyway.**

**Episode 2 (Or Episode 97): Déjà ****Vu Again?**

Over the next couple of weeks, Aelita slowly recovered back to health. She could speak again and the pain had nearly gone away. Apart from pain in her heart. She still felt alone. Her friends had tried to comfort her but she didn't want their pity.

Jeremie had being staying at the lab most of the time. He was still trying to work out what Xana had taken from Aelita. He was also searching for Franz Hopper. Jeremie owed a great deal to Franz and wanted to return the favour. The search he had started returned with zero. He wondered about the possibilities of Franz surviving. It didn't look good.

_A __Replika__._ _This is all that remains of a vast Xana Empire?_ the Dark Warrior thought to himself. This was still a perfect staging ground for the final phase of Xana's Legacy. Xana knew he would meet his demise, so he created this Xana Warrior and told him the plan. In the event of Xana's unfortunate passing away, then he would need 3 things in order to proceed. He needed a copy of the Keys to Lyoko. He used to have them and even used them but they were destroyed, when he thought he didn't need them. While Franz transferred his energy to the program (Which would eventually kill Xana), Xana barely managed to get a copy of his set of the keys and transfer them to his Warrior.

But the warrior still needed the other set of Keys. He managed to get a copy from Miss Stones. The original plan was to just take the real keys and let Aelita die. The dark warrior had other plans. He wanted Aelita to see what Xana had been planning all along. The third thing was a sample of Xana, which came in the form of the warrior himself. He didn't like the fact that he had to sacrifice himself but Xana demanded it, so he shall obey.

Odd lay on his bed, staring at the ceiling, thinking. He was worried about Aelita. She hadn't eaten for days and she was ignouring them. Aelita was so depressed about the though of having no family, that she had isolated herself from the rest of the group! Ulrich then came in, and sat down on his bed.

"Spoken to Aelita yet?" asked Ulrich. They were all worried about Aelita.

"No, have you?" responded, Odd hopefully. Ulrich just shook his head. Odd wonder if this had anything to do with the Xana Warrior.

"Have you heard back from Jeremie? Has he found anything?" Odd asked, still thinking about what had happened.

"He hasn't found anything so far." Ulrich knew that Aelita meant a lot to Odd. They were almost like Brother and Sister. It was that close. "But I don't think Aelita acting like this has anything to do with what Xana did to her. I think she's depressed because she has no relatives left in the world."

"But she still has us."

"That's not really the same as having real relatives."

Odd sighed. Ulrich had a point. Aelita wanted to have a family she could talk to and they weren't substitutes. Odd then went back to staring at the ceiling, hoping Aelita would be okay at the end of this.

Jeremie was still searching for Franz Hopper, when he noticed something. The Superscan displayed a Replika! It was charging up energy. What its use or purpose was, he didn't know, but he knew it was trouble. Jeremie quickly called Aelita. She immediately hanged up on him. He didn't blame her. She had just lost her family! Jeremie then phoned Ulrich.

"Ulrich, I need you to get Odd and meet me over at the factory."

"Problem?" questioned Ulrich, already knowing the answer.

"Just get here. I'll explain it once you're at the factory."

"Ok. We're on our way." Ulrich then hanged up. He turned to Odd.

"Something happening at the factory. Possibly Xana."

Odd immediately got up and rushed to the door.

"Ok, let's go!"

Jeremie glanced at the display. The charging level of the Replika was now reaching 70%. _Where are they? _he thought. Then as if on cue, Ulrich, Yumi and Odd entered the Lab.

"So what's the problem, Einstein?" asked Odd, walking over to the interface.

"A Replika is charging up massive amounts of energy and whatever it is, it can't be good. I'm going to need you to go to the Replika and find out what's going on." Jeremie was worried. Considering who was controlling the Replika, the charging energy wasn't a good sign.

"And just how are we supposed to get there?" Yumi responded. "We don't have the Skid anymore, remember."

"I've been working on a program, in case the fight went on a little longer. If we lost the Skid, this program allows me to virtualize you guys straight onto the Replika."

"You just decided to tell us now?"

"Well, we didn't need a program like this until now."

"Is it safe?" questioned Ulrich, remembering the time he became a spectre.

Jeremie hesitated. "Uhh… this would be the first time it's tested."

Ulrich sighed. This was the problem about not fighting Xana for a long time. If this were back in the old days, Jeremie would have had this program ready and tested.

"Well it's the best we've got, so better make use of it." Ulrich responded and started to wonder what he had gotten himself into.

On the Replika, a pillar of blood red light erupted skywards. The Dark Warrior watched eagerly. Soon Xana would rise again. Then something caught the Warrior's attention. He looked around and then smiled.

Three beings came into existence above the Replika.

"It looks like I have guests." He said to himself. "And to think, I thought I would be bored…"

He ran off towards the newcomers, sword in hand.

Aelita walked out of her room into the corridor. As she closed the door, William walked up to her. _Oh no. _she thought to herself. _Not more pity. Why can't they understand, I just want to be alone._

"Aelita, I wanted to talk." William had a look of concern on his face.

"Leave me alone." forcefully responded Aelita. She was about to walk away, when William blocked her path.

"Aelita. I've been watching you fall apart for the last couple of weeks now. You don't even talk to your friends anymore! Now, what happened?"

"I don't want to talk about it! Now let me through." Aelita was annoyed that it seemed everybody was trying to consoling her. She just wanted to be left alone!

"No." said William standing his ground. "I won't let you through, until you tell me!"

"Why can't people see that I want to be alone?!" shouted Aelita as she broke down into tears.

"It's ok, Aelita. You can tell me." said William sympathetically. "How about you come back to my room and explain what happened?"

Aelita looked at him. William wasn't such a bad guy once you got to know him.

"Ok." she reluctantly agreed. "Maybe I do need to talk to someone."

Ulrich's feet landed on the Ice Replika. He let out a sigh of relief. The program had worked and he wasn't dead!

"Jeremie, it worked!" Ulrich shouted to the sky, as he watched Yumi and Odd land. "We're all here and in good condition!"

"You doubted me?" responded Jeremie with a hint of surprise in his voice.

"Not normally, but this time you had me pretty worried!"

Yumi was looking over at the distant horizon.

"Hey, check it out!" She said, while pointing at the large pillar of red energy.

"Wow! Einstein is that the energy that you're superscan detected?" asked Odd, staring at the pillar.

"Yes. According to the readings, it's charged to 85%. You need to get going!" Jeremie still wondered what Xana was doing. There wasn't enough energy to summon another Kolossus, so what was he planning?

"Ok, but we need the Overvehicles!"

"Sorry no can do, Odd. Since there's no Skid, I can't send weapons or vehicles. You're on your own."

"Well, what are we waiting for?" responded Odd running on four legs. Yumi and Ulrich then took off after him.

As the Lyoko warriors ran towards the pillar of energy, they were being stalked by a river of black smoke. Ulrich was running ahead of the others. This was the Dark Warriors time to strike. Yumi noticed the black smoke catching up with Ulrich.

"Ulrich, Look out!!" She shouted but was too late.

The Xana Warrior jumped out of the smoke. Ulrich just caught a glimpse of the Warrior. The Dark Warrior came in with his barbed broadsword. Ulrich drew his Katana to defend. The powerful blow struck. Ulrich smashed into the icy rock face. The Warrior then got hit 4 times in the arm. He turned and saw Odd, who was still aimed directly at him. The Dark Warrior dug his sword deep in the Replika. A beam of red lightening came racing out towards Odd.

"That's a new trick!" shouted Odd helplessly as the lightening struck. He was sent flying a good couple of feet backwards.

"I'm always full of new tricks, Mr. Della Robbia!" responded the Xana Warrior as odd land on the ground. "Unfortunately, I can't say the same thing for you!" He started to stroll towards the downed Odd. "But I must say that one thing surprises me." He then looked down at the felled Lyoko Warrior. "Where is the Princess? I was hoping for her to see my grand ascension!" The warrior then stood one foot on Odd. "Where is Miss Stones?" Before Odd could say a word, the Xana Warrior was sent flying across the Replika surface. The two fans returned to their owner. As the Dark Warrior got up, he saw two Tennsin fans directly at his neck.

"Xana won't succeed today!" said Yumi glaring at him. The warrior turned and saw the pillar of light. It was almost complete!

"Oh look at the time! I have an appointment with destiny and I can't be late!" He responded and disappeared into dark smoke. Yumi looked around surprised, but she couldn't find him.

"Jeremy, I lost him" Yumi shouted to the sky. What was the warrior planning?

"Yumi, he's heading towards the energy pillar. You've got to stop him!" ordered Jeremie. He knew that the Xana Warrior was doing all this for a purpose.

Yumi turned and saw Ulrich get up out of his mold in the ice wall.

"Let's get moving!" He said in slight discomfort. Yumi just nodded. Odd finally got up from the blast and followed Yumi and the Super Sprinting Ulrich towards the pillar of light.

The Xana Warrior had finally reached the base of the pillar of energy. He looked around one last time. A shame really, him having to give up his life! But orders were orders.

"STOP!" shouted Ulrich as finally reached him. Ulrich withdrew his Katana.

"You're too late! Xana has won!!" shouted Dark Warrior manically. He then jumped into the energy. Ulrich raced forward to try and stop him. There was blinding flash and both the Warrior and the pillar vanished. Just then, Odd and Yumi arrived on the scene.

"Sorry Jeremie, I couldn't stop him!" responded Ulrich staring at where the warrior had previously been. Jeremie sat in silence and thought about what had just happened. What was Xana's plan?

Aelita walk out of William's room, feeling a bit better. She turned to face William.

"Aelita, I know you went through a tough time but it does help to talk about your problems." said William. Aelita nodded.

"I guess I was just so worked up about it, I didn't feel I could talk to anybody about my problems." she admitted.

"It's ok. If you ever need someone to talk to, you can talk to me and I'll listen." At this, Aelita smiled. They walked along the corridor together. Then Aelita walk on to the elevator and leaned against the wall for support. She felt as though she had just been devirtualized. She looked up weakly.

"Huh?" she looked around puzzled. "Déjà vu?"

To be continued in part 2!

**Authors Note: ****Yep I'm evil creating that cliffhanger! So what's happened with Aelita? There hasn't been a return to the past activated. So what's Xana's plan? Well you'll just have to wait for part 2!**


End file.
